Extended Data Fig. 7: Reference (10x) and query (Smart-seq2) single-cell RNA sequencing datasets characterizing the single-cell transcriptomes of microglia.
From: Directed evolution of adeno-associated virus for efficient gene delivery to microglia
a,d, Quantification of gene counts, UMI counts, the percentage of mitochondria RNA, and the percentage of ribosome RNA in the query (a) and the reference (d) datasets. Red dots represent sequenced microglia that failed to pass the quality check and were removed from subsequent analysis. b,e, UMAP plot of all cells (left and middle) and filtered microglia (right) sequenced using the Smart-seq2 protocol (b) or 10x Genomics platform (e). The blue color in the left panel indicates Hexb expression level. Cells with high Hexb expression (red in the middle panel) were identified as microglia and retained for subsequent analysis. c, Violin plots showing the UMI counts and the number of detected genes in the reference and the query datasets. f,g, Gene expression analysis of the query (f) and the reference (g) datasets. The heatmap shows the z-score of relative gene expression. The violin plots show the expression level of homeostatic marker genes (P2ry12, Cx3cr1, Sall1 and Csf1r) and reactive marker genes (Il1b, Spp1, Ifitm3 and Ccl5).
